Gethin Jones' low strike from 20 yards early in the second-half settled the contest in Wanderers' favour.
The Lancashire FA headquarters was packed for the clash, this the first time North End had seen their team live since March 2020.
It was a generally disjointed display from North End, an improvement seen when they made outfield changes later in the second half.
In the first half they were indebted to keeper Connor Ripley for making a string of good saves to keep the game goalless going into the interval.
Within five minutes of the restart, Ripler's half-time replacement Mathew Hudson was beaten by Jones' good finish.
PNE's best chance was a shot from first-half sub Ethan Walker which clipped the outside of the far post.
North End played in a 3-5-2 system, Joe Rafferty and Jack Baxter operating at wing-backs either side of Sepp van den Berg, Patrick Bauer and Josh Earl.
Second-year scholar Lewis Leigh partnered Tom Bayliss in midfield, with Brad Potts operating higher up the pitch.
Scott Sinclair played up front with Sean Maguire.
Free-kicks provided the first sight of goal for both teams, Leigh putting an early one into the wall while at the other end, Connor Ripley saved from Xavier Amaechi.
Potts scuffed a shot wide from the edge of the box after being teed-up by Sinclair, while Patrick Bauer got up high to meet a Bayliss free-kick from the left but headed over.
There was a busy spell for Ripley as Bolton got on top of the game and enjoyed a good spell of pressure.
In the 39th minute, he got down to parry a shot from Jones, with Oladapo Afoayan scooping the rebound over the bar.
Ripley, playing his first pre-season game, got a touch to Jones' cross shot to take it behind, then soon afterwards produced a splendid double save to keep the score level.
He dived to his right to get a hand to Josh Sheehan's shot, then got up to block the follow-up from Antoni Sarcevic.
North End responded with a chance of their own just before half-time, Maguire driving through the middle of the pitch before slipping a pass outside toWalker who had replaced Baxter.
Walker cut inside from the left-wing on to his right foot and hit a shot across goal which clipped the outside of the far post on its way wide.
That shot aside, Bolton had been the better side towards the end of the first half and they carried that into the second half, opening the scoring in the 51st minute.
North End didn't clear their lines fully after a Bolton attack and when the ball fell to Jones 20 yards out, he drilled a low shot past Hudson who was rooted to the spot.
Hudson denied Afoayan extending Bolton's lead four minutes later, leaping backwards to tip the striker's shot over the bar.
There was a coming together of a number of players when Leigh caught Jones with a challenge, Jones reacting angrily to it.
Referee Jeremy Simpson calmed the situation with the help of his assistants and showed both players a yellow card.
Maguire had a shot from the edge of the box which lacked power, the Bolton keeper diving to save although it was going wide.
North End made 10 outfield substitutions after 67 minutes, giving the side a much stronger look.
Among those coming on was 16-year-old Noah Mawene, playing behind the front two.
They were better for the subs, looking more of a threat going forward in the closing stages.
PNE's best chance of an equaliser came when Emil Riis chased a ball down the side of the box and showed some neat footwork to turn it back into the middle for Ched Evans who couldn't meet it cleanly
PNE: Ripley (Hudson 46), van den Berg (Storey 67), Bauer (Lindsay 67), Earl (Hughes 67), Rafferty (Cunningham 67), Bayliss (Ledson 67), Leigh (Whiteman 67), Potts (Mawene 67), Baxter (Walker 35, Barkhuizen 67), Sinclair (Riis 67), Maguire (Evans 67).
Dixon, Jones (Brockbank 62), Almeida Santos, Baptiste, Gordon, Sheehan, Williams, Sarcevic, Amaechi (Delfouneso 21), Afoayan, Bakayoko. Subs: Hutchinson, Senior, Aimson, Conway, Thomason, Titte, Darcy.
Referee: Jeremy Simpson (Carnforth)